Nasal administration of anti-CD3 monoclonal antibody (Foralumab) modulates effector CD8+ T cell function and induces a regulatory response in T cells in human subjects
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE217357 | GEO | 2022/11/05
REPOSITORIES: GEO
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Project description:Purpose: The aim of this study is the evaluation of differential gene expression profile by RNA-seq in response to anti-CD3 treatment in CD3 cells obtained from blood samples of healthy donors, to achieve a better understanding of the antibodies molecular mechanisms of action. In this study T cells were treated in the complex PBMC milieu, in a tentative to mimetize the natural ambient that occurs in a clinical administration of therapeutic anti-CD3. Methods: Human peripheral blood mononuclear cells were purified from healthy volunteers blood and were cultured in the presence of the monoclonal antibody OKT3 or a recombinant fragment of humanized anti-CD3 (FvFcR) or recombinant fragment chimeric anti-CD3 (FvFcM). After 72 hours, CD3+ T cells were isolated by negative selection using magnetic beads and total RNA was extracted with the RNeasy kit (Qiagen). Paired-end cDNA reads (150bp) were generated using the HiSeq 2500 Sequencing system (Illumina) located at the NGS Overseas Project Manager, Next Generation Sequencing Division, Macrogen, Inc. (Seoul, Korea). Quality check of the paired-end reads was performed using FASTQC. The reads were aligned to the human genome refence downloaded from the UCSC Genome Browser database using open source segemehl_0_2_0. The aligned files were ordered and indexed using Samtools followed by read count using HTSeq-count. Statistical analysis was done using the R environment for statistical computing. Gene model quantification were performed using the Bioconductor package DESeq2. Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the human genome and identified 7089 transcripts in the T cell stimulated with OKT3, 2425 transcripts with FvFc R and 1406 with FvFc M. RNA-seq data confirmed stable expression of some known housekeeping genes, and 3 of these were validated with qRT-PCR. We found 860 genes there are equally regulated among the treatments, considering a padj ≤ 0.05. Altered expression of 35 genes was confirmed with qRT-PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: In conclusion, we had used a deep transcriptome sequencing method for comparing three anti-CD3 antibodies in terms of gene ontology enrichment and immunological markers expression. The present data showed that both recombinant antibodies induced a compatible expression profile, suggesting they could be tested as substitute in human pre-clinical trials. Moreover, the proposed methodology is amenable to be more generally applied for molecular comparison purposes.
2019-08-07 | GSE112899 | GEO
Project description:KY1044 is a human monoclonal IgG1 that selectively binds to Inducible T cell CO-stimulator (ICOS). The co-stimulatory effect of KY1044-stimulated human T cells was analysed by RNA sequencing (RNA seq). Purified pre-activated (ICOS+ve) T cells were stimulated with either KY1044 and anti-CD3 or anti-CD3 alone and cells were harvested for RNA seq after 6hrs. Kallisto transcript abundance are provided in the absence of raw sequence reads.
2020-09-01 | E-MTAB-9500 | biostudies-arrayexpress
Project description:CD3-bispecific antibodies represent an important therapeutic strategy in oncology. These molecules work by redirecting cytotoxic T cells to antigen-bearing tumor cells. Although CD3-bispecific antibodies have been developed for several clinical indications, cases of cancer-derived resistance are an emerging limitation to the more generalized application of these molecules. Here, we devised whole-genome CRISPR screens to identify cancer resistance mechanisms to CD3-bispecific antibodies across multiple targets and cancer types. By validating the screen hits, we found that deficiency in IFNγ signaling has a prominent role in cancer resistance. Interestingly, IFNγ functions by stimulating the expression of T cell killing-related molecules in a cell type-specific manner. Additionally, by assessing resistance to the clinical CD3-bispecific antibody flotetuzumab, we identified core fucosylation as a novel and critical pathway to regulate flotetuzumab binding to the CD123 antigen. Disruption of this pathway resulted in significant resistance to flotetuzumab treatment. Moreover, proper fucosylation of CD123 is required for its normal biological functions. In order to treat the resistance associated with fucosylation loss, flotetuzumab in combination with an alternative targeting CD3-bispecific antibody demonstrated superior efficacy. Together, our study reveals multiple mechanisms that can be targeted to enhance the clinical potential of current and future T cell engaging CD3-bispecific antibody therapies.
2020-11-12 | GSE159547 | GEO
Project description:This study investigated temporal transcriptomic changes in response to nasal allergen challenge of titrated timothy grass pollen. This is an open single-center observational study conducted outside the pollen season. Twelve participants with seasonal allergic rhinitis underwent a control (diluent) challenge followed by nasal allergen challenge after an interval of 14 days. On each challenge day, nasal challenge with control or titrated timothy grass pollen (Aquagen, phleum pratense; ALK) was administered. Peripheral blood was collected before nasal challenge (baseline) and at 3, 6 and 24 hours following challenge. RNA was extracted from whole blood and CD4 cells for microarray experiment using Affymetrix Human Gene 1.0 ST arrays.
2013-01-16 | E-GEOD-43497 | biostudies-arrayexpress
Project description:The tolerogenic anti-CD3 monoclonal antibodies (anti-CD3) are promising compounds for the treatment of type 1 diabetes (T1D). Anti-CD3 administration induces transient T-cell depletion both in preclinical and in clinical studies. Notably, said depletion mainly affects CD4+ but not CD8+ T cells. Moreover, T1D reversal in preclinical models is accompanied by the selective expansion of CD4+FOXP3+ T regulatory (Treg) cells, which are fundamental for the long-term maintenance of anti-CD3-mediated tolerance. The mechanisms that lead to this immune-shaping by affecting mainly CD4+ T effector cells while sparing CD4+FOXP3+ Treg cells have still to be fully elucidated. This study shows that CD3 expression levels differ from one T-cell subset to another. CD4+FOXP3- T cells contain higher amounts of CD3 molecules than do CD4+FOXP3+ and CD8+ T cells both in mice and in humans. Said differences may explain the anti-CD3-mediated immune resetting that occurs in vivo after anti-CD3 administration in mice. In addition, transcriptome analysis demonstrates that CD4+FoxP3+ Treg cells are significantly less responsive than CD4+FoxP3- T cells to anti-CD3 treatment at molecular levels. Thus, heterogeneity in CD3 expression likely confers the various T-cell subsets differing susceptibility to in vivo tolerogenic anti-CD3-mediated modulation. This data sheds new light on the molecular mechanism that underlies anti-CD3-mediated immune resetting, and thus may open new opportunities to improve this promising treatment.
2015-01-19 | E-MTAB-2437 | biostudies-arrayexpress
Project description:We have developed a monoclonal antibody (mAb) C7 that reacts with Als3p and enolase present in Candida albicans cell wall and exerts three anti-Candida activities: candidacidal activity and inhibition of both adhesion and filamentation. To investigate the mode of action of mAb C7 on fungal viability, we examined changes in the genome-wide gene expression profile of C. albicans grown in presence of a subinhibitory concentration of mAb C7 (12.5 µg/ml) by using microarrays. A total of 49 genes were found to be differentially expressed upon treatment with mAb C7. Of these, 28 were found to be up-regulated and 21 down-regulated. The categories of up-regulated genes with the largest number of variations were those involved in iron uptake or related to iron homeostasis (42.86%), while the energy-related group accounted for 38.10% of the down-regulated genes (8/21). Results were validated by real Time PCR. Since these effects resembled those found under iron-limited conditions, the activity of mAb C7 on C. albicans mutants with deletions in key genes implicated in the three iron acquisition systems described in this yeast was also assessed. Only mutants lacking TPK1 and TPK2 genes were less sensitive to the candidacidal effect of mAb C7. FeCl3 or hemin at concentrations ≥ 7.8µM reversed the candidacidal effect of mAb C7 on C. albicans, on a concentration dependent manner. The results presented in this study provide evidence that the candidacidal effect of mAb C7 is related to the blockage of the reductive iron uptake pathway of C. albicans. A saturated culture of C. albicans grown overnight was diluted to an optical density at 600 nm of approximately 0.1 and divided in two aliquots. One of them was used untreated as control and the second one was treated with a subinhibitory concentration (12.5 µg/ml) of monoclonal antibody C7 . Both cultures were incubated for 18 h at 37ºC before harvesting cells. Antibody added and control samples were obtained each time. The experiment was repeated once. Dye-swap technique was used for hybridization and four arrays were analyzed to compare the expresion of over six thousands genes in response to antibody C7.
2010-12-11 | E-GEOD-25969 | biostudies-arrayexpress
Project description:We performed a global gene expression analysis comparing intragraft tolerant CD8+ T cells from CD3 antibody-treated mice showing permanent islet graft survival to intra-graft effector CD8+ T cells isolated from untreated mice showing acute rejection of islet allografts. The objective was to emphasize the anergic profile of CD8+ T cells residing within the pancreatic islet allograft of mice rendered tolerant following CD3 antibody therapy.
2017-02-10 | GSE68208 | GEO
Project description:In this study, based on microarray hybridization and the detections of RTqPCR and Western Blotting, we have shown that HeLa cells treated with LHRH receptor monoclonal antibody 4F3B10 increased protein expressions in Fas signaling pathway, which provided a novel route for the gene therapy of HeLa cells.
2017-03-06 | GSE95695 | GEO
Project description:The characteristics of monoclonal antibodies (mAbs) cohering various function effectors shows great expectation in therapy. Glycosylation, one of the common post-translational modifications, deeply influences the cohesion. It is necessary to grasp monosaccharide composition/sequence and glycan structures in mAbs. There have been comprehensive mass spectrometry characterization of N-glycosylation of mAbs, and monosaccharide compositions are deduced according to known biosynthetic rules. Our recently developed intact N-glycopeptide search engine GPSeeker has made unambiuous structure-specific characterization of N-glycosylation possible with structure-diagnostic fragment ions from selective fragmentattion of N-glycan moieties.
2022-04-14 | PXD032275 | Pride
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2024-02-15 | GSE247376 | GEO